European higher education institutions (HEIs) in the last two decades have faced a number of challenges: reduced public funding, increased competition from foreign and private universities, constant pressures and demands for their greater quality, and constant changes of education laws and legal regulations. The only way for fast adjustment of HEIs to the new competitive conditions is to explore all possibilities for effective implementation of some of the most popular management concepts such as Balanced Scorecard (BSC) system. Although the application of the BSC in the business sector is well documented, limited research has been reported regarding the application of the BSC in the education sector. For this purpose, relied on the existing literature, reported results and experiences from its implementation in business, firstly, we propose a suitable process for building a BSC system for HEI, and then we design a specific Strategy map and BSC system applicable for the Faculty of Economics-Skopje, Ss. Cyril and Methodius University, easily adaptable for implementation in other HEIs.